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For: Hou X, Yang Y, Li P, Zeng Z, Hu W, Zhe R, Liu X, Tang D, Ou M, Dai Y. Integrating Spatial Transcriptomics and Single-Cell RNA-seq Reveals the Gene Expression Profling of the Human Embryonic Liver. Front Cell Dev Biol 2021;9:652408. [PMID: 34095116 PMCID: PMC8173368 DOI: 10.3389/fcell.2021.652408] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 04/26/2021] [Indexed: 11/14/2022]  Open
Number Cited by Other Article(s)
1
Li SY, Liu ST, Wang CY, Bai YZ, Yuan ZW, Tang XB. Comprehensive circRNA expression profile and hub genes screening during human liver development. Ann Med 2025;57:2497111. [PMID: 40285372 PMCID: PMC12035923 DOI: 10.1080/07853890.2025.2497111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/12/2024] [Revised: 01/08/2025] [Accepted: 01/31/2025] [Indexed: 04/29/2025]  Open
2
Miao X, Huang Y, Ge KX, Xu Y. Application of scRNA-seq in Dental Research: Seeking Regenerative Clues From the Structure of Tooth and Periodontium in Physical or Pathological States. FRONT BIOSCI-LANDMRK 2025;30:26200. [PMID: 40018926 DOI: 10.31083/fbl26200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2024] [Revised: 10/14/2024] [Accepted: 10/31/2024] [Indexed: 03/01/2025]
3
Ou J, Zeng H, Shangguan Y, Luan S, Wu H, Li H, Gong W, Tang D, Tan X, Yin L, Dai Y. Exploring the Spatial Distribution of Interstitial Cells in Kidney Tissue. Kidney Blood Press Res 2024;50:1-13. [PMID: 39527920 DOI: 10.1159/000542501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2024] [Accepted: 11/04/2024] [Indexed: 11/16/2024]  Open
4
Matchett KP, Paris J, Teichmann SA, Henderson NC. Spatial genomics: mapping human steatotic liver disease. Nat Rev Gastroenterol Hepatol 2024;21:646-660. [PMID: 38654090 DOI: 10.1038/s41575-024-00915-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/28/2024] [Indexed: 04/25/2024]
5
Shui L, Maitra A, Yuan Y, Lau K, Kaur H, Li L, Li Z, Translational and Basic Science Research in Early Lesions (TBEL) Program. PoweREST: Statistical Power Estimation for Spatial Transcriptomics Experiments to Detect Differentially Expressed Genes Between Two Conditions. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.30.610564. [PMID: 39257799 PMCID: PMC11384012 DOI: 10.1101/2024.08.30.610564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2024]
6
Wang H, Liu J, Zhu P, Shi L, Liu Y, Yang X, Yang X. Single-nucleus transcriptome reveals cell dynamic response of liver during the late chick embryonic development. Poult Sci 2024;103:103979. [PMID: 38941785 PMCID: PMC11261130 DOI: 10.1016/j.psj.2024.103979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 05/29/2024] [Accepted: 06/10/2024] [Indexed: 06/30/2024]  Open
7
Ahamed F, Eppler N, Jones E, Zhang Y. Understanding Macrophage Complexity in Metabolic Dysfunction-Associated Steatotic Liver Disease: Transitioning from the M1/M2 Paradigm to Spatial Dynamics. LIVERS 2024;4:455-478. [PMID: 39328386 PMCID: PMC11426415 DOI: 10.3390/livers4030033] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 09/28/2024]  Open
8
Agrawal H, Mehatre SH, Khurana S. The hematopoietic stem cell expansion niche in fetal liver: Current state of the art and the way forward. Exp Hematol 2024;136:104585. [PMID: 39068980 DOI: 10.1016/j.exphem.2024.104585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2024] [Revised: 07/18/2024] [Accepted: 07/19/2024] [Indexed: 07/30/2024]
9
Yan C, Zhu Y, Chen M, Yang K, Cui F, Zou Q, Zhang Z. Integration tools for scRNA-seq data and spatial transcriptomics sequencing data. Brief Funct Genomics 2024;23:295-302. [PMID: 38267084 DOI: 10.1093/bfgp/elae002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 09/26/2023] [Accepted: 01/03/2024] [Indexed: 01/26/2024]  Open
10
Fujiwara N, Kimura G, Nakagawa H. Emerging Roles of Spatial Transcriptomics in Liver Research. Semin Liver Dis 2024;44:115-132. [PMID: 38574750 DOI: 10.1055/a-2299-7880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 04/06/2024]
11
Chen G, Xu W, Long Z, Chong Y, Lin B, Jie Y. Single-cell Technologies Provide Novel Insights into Liver Physiology and Pathology. J Clin Transl Hepatol 2024;12:79-90. [PMID: 38250462 PMCID: PMC10794276 DOI: 10.14218/jcth.2023.00224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 06/25/2023] [Accepted: 07/12/2023] [Indexed: 01/23/2024]  Open
12
Zhu JH, Guan XC, Yi LL, Xu H, Li QY, Cheng WJ, Xie YX, Li WZ, Zhao HY, Wei HJ, Zhao SM. Single-nucleus transcriptome sequencing reveals hepatic cell atlas in pigs. BMC Genomics 2023;24:770. [PMID: 38087243 PMCID: PMC10717992 DOI: 10.1186/s12864-023-09765-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 10/24/2023] [Indexed: 12/18/2023]  Open
13
Zhu X, Pang L, Ding X, Lan W, Meng S, Peng X. A Gene Correlation Measurement Method for Spatial Transcriptome Data Based on Partitioning and Distribution. J Comput Biol 2023;30:877-888. [PMID: 37471241 DOI: 10.1089/cmb.2023.0108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/22/2023]  Open
14
Kang HM, Lee JH. Spatial Single-Cell Technologies for Exploring Gastrointestinal Tissue Transcriptome. Compr Physiol 2023;13:4709-4718. [PMID: 37358516 PMCID: PMC10386894 DOI: 10.1002/cphy.c210053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/27/2023]
15
Du J, Yang YC, An ZJ, Zhang MH, Fu XH, Huang ZF, Yuan Y, Hou J. Advances in spatial transcriptomics and related data analysis strategies. J Transl Med 2023;21:330. [PMID: 37202762 PMCID: PMC10193345 DOI: 10.1186/s12967-023-04150-2] [Citation(s) in RCA: 56] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 04/25/2023] [Indexed: 05/20/2023]  Open
16
Bomfim BCM, Azevedo-Silva J, Caminha G, Santos JPR, Pelajo-Machado M, de Paula Ayres-Silva J. Lectin-based carbohydrate profile of megakaryocytes in murine fetal liver during development. Sci Rep 2023;13:6729. [PMID: 37185919 PMCID: PMC10130079 DOI: 10.1038/s41598-023-32863-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Accepted: 04/04/2023] [Indexed: 05/17/2023]  Open
17
Choe K, Pak U, Pang Y, Hao W, Yang X. Advances and Challenges in Spatial Transcriptomics for Developmental Biology. Biomolecules 2023;13:biom13010156. [PMID: 36671541 PMCID: PMC9855858 DOI: 10.3390/biom13010156] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 12/15/2022] [Accepted: 12/17/2022] [Indexed: 01/15/2023]  Open
18
Fan Z, Luo Y, Lu H, Wang T, Feng Y, Zhao W, Kim P, Zhou X. SPASCER: spatial transcriptomics annotation at single-cell resolution. Nucleic Acids Res 2023;51:D1138-D1149. [PMID: 36243975 PMCID: PMC9825565 DOI: 10.1093/nar/gkac889] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 09/21/2022] [Accepted: 10/13/2022] [Indexed: 01/30/2023]  Open
19
Milanese JS, Marcotte R, Costain WJ, Kablar B, Drouin S. Roles of Skeletal Muscle in Development: A Bioinformatics and Systems Biology Overview. ADVANCES IN ANATOMY, EMBRYOLOGY, AND CELL BIOLOGY 2023;236:21-55. [PMID: 37955770 DOI: 10.1007/978-3-031-38215-4_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/14/2023]
20
Duan H, Cheng T, Cheng H. Spatially resolved transcriptomics: advances and applications. BLOOD SCIENCE 2023;5:1-14. [PMID: 36742187 PMCID: PMC9891446 DOI: 10.1097/bs9.0000000000000141] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 10/19/2022] [Indexed: 11/06/2022]  Open
21
Hou X, Wang YL, Shi W, Hu W, Zeng Z, Liu J, Li L, Cai W, Tang D, Dai Y. Multiplexed analysis of gene expression and chromatin accessibility of human umbilical cord blood using scRNA-Seq and scATAC-Seq. Mol Immunol 2022;152:207-214. [DOI: 10.1016/j.molimm.2022.10.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 10/21/2022] [Accepted: 10/25/2022] [Indexed: 11/13/2022]
22
Lee IS, Takebe T. Narrative engineering of the liver. Curr Opin Genet Dev 2022;75:101925. [PMID: 35700688 PMCID: PMC10118678 DOI: 10.1016/j.gde.2022.101925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Revised: 05/06/2022] [Accepted: 05/08/2022] [Indexed: 11/30/2022]
23
Hou X, Hong X, Ou M, Meng S, Wang T, Liao S, He J, Yu H, Liu L, Yin L, Liu D, Tang D, Dai Y. Analysis of Gene Expression and TCR/B Cell Receptor Profiling of Immune Cells in Primary Sjögren's Syndrome by Single-Cell Sequencing. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2022;209:238-249. [PMID: 35705251 DOI: 10.4049/jimmunol.2100803] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 04/18/2022] [Indexed: 01/07/2023]
24
Chen L, Li J, Yuan R, Wang Y, Zhang J, Lin Y, Wang L, Zhu X, Zhu W, Bai J, Kong F, Zeng B, Lu L, Ma J, Long K, Jin L, Huang Z, Huo J, Gu Y, Wang D, Mo D, Li D, Tang Q, Li X, Wu J, Chen Y, Li M. Dynamic 3D genome reorganization during development and metabolic stress of the porcine liver. Cell Discov 2022;8:56. [PMID: 35701393 PMCID: PMC9197842 DOI: 10.1038/s41421-022-00416-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 04/28/2022] [Indexed: 11/28/2022]  Open
25
Friedman SL, Pinzani M. Hepatic fibrosis 2022: Unmet needs and a blueprint for the future. Hepatology 2022;75:473-488. [PMID: 34923653 DOI: 10.1002/hep.32285] [Citation(s) in RCA: 250] [Impact Index Per Article: 83.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 11/12/2021] [Accepted: 11/15/2021] [Indexed: 12/12/2022]
26
Gifre-Renom L, Daems M, Luttun A, Jones EAV. Organ-Specific Endothelial Cell Differentiation and Impact of Microenvironmental Cues on Endothelial Heterogeneity. Int J Mol Sci 2022;23:ijms23031477. [PMID: 35163400 PMCID: PMC8836165 DOI: 10.3390/ijms23031477] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 01/14/2022] [Accepted: 01/19/2022] [Indexed: 02/04/2023]  Open
27
Liang R, Lin YH, Zhu H. Genetic and Cellular Contributions to Liver Regeneration. Cold Spring Harb Perspect Biol 2021;14:a040832. [PMID: 34750173 PMCID: PMC9438780 DOI: 10.1101/cshperspect.a040832] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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